walking the cattle continuum moving from the bovinesnp50 to higher and lower density snp panels
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Walking the Cattle Continuum: Moving From the BovineSNP50 to Higher- and Lower-Density SNP Panels. Introduction. The Illumina Bovine SNP50 Bead Chip has been very successful A new high-density chip with 778K markers is now available A low-density chip with 3K markers will be available soon

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introduction
Introduction
  • The Illumina Bovine SNP50 Bead Chip has been very successful
  • A new high-density chip with 778K markers is now available
  • A low-density chip with 3K markers will be available soon
  • Other densities under development
bovine snp50 bead chip
Bovine SNP50 Bead Chip
  • The Illumina Bovine SNP50 Bead Chip has been very successful
  • 43,382 SNP used for genetic prediction
  • 47,645 animals genotyped in the US, many more worldwide
  • 2nd generation chip with a slightly different SNP set has been developed
uses of the snp50
Uses of the SNP50
  • Genetic improvement
    • Genomic prediction
    • Parentage and breed confirmation
  • Scientific research
    • Improving the assembly
    • QTL discovery (calving traits, SCS)
      • Recessives and causative mutations
    • Phylogeny
genotyped holsteins august 2010
Genotyped Holsteins August 2010

*Traditional evaluation

**No traditional evaluation

rel for young holstein bulls july 2010

5000

4500

4000

Bulls (no.)

3500

3000

2500

2000

1500

1000

500

0

60

61

64

65

66

67

68

69

70

71

72

73

74

75

76

77

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79

80

REL (%) for mlk yield

REL for young Holstein bulls July 2010
bovine high density bead chip hd
Bovine High-Density Bead Chip (HD)
  • 778K SNP chosen to
    • Be evenly spaced
    • Include some Y-specific SNP
    • Include mitochondrial SNP
  • Utilize across-breed information
  • Fine mapping of QTL
  • Enhanced performance in Zebu cattle
collaboration was essential
Collaboration was essential
  • University of Missouri
  • Roslin Institute
  • UNCEIA (France)
  • Sao Paulo State University
  • University of Milan
  • Technische Universitaet Muenchen
  • Beef CRC
  • Embrapa
  • National University (Korea)
  • Illumina provided:
    • DNA sequence for a range of breeds
  • Pfizer provided:
    • DNA sequence of additional breeds
    • SNP discovery expertise
  • USDA-ARSprovided:
    • DNA and library construction
    • SNP discovery expertise
    • Assay design expertise
data highlights
Data highlights
  • Enormous amount of DNA sequence data
    • ~180-200x genome equivalent coverage
    • ~600 BILLION base-pairs
  • Represents:
    • ~120 libraries
    • >300 animals
  • Animals from breeds representing:
    • European and Zebu cattle
    • Beef and dairy
    • Temperate and tropically adapted
slide11

Partners

Deep SNP Discovery

N’Dama

Sahiwal

Simmental

Hanwoo

Blonde d’Aquitaine

Montbeliard

BFGL

Genome Assemblies

Nelore

Water Buffalo

BFGL-Illumina

Deep SNP Discovery

Angus

Holstein

Limousin

Jersey

Nelore

Brahman

Romagnola

Gir

Pfizer

Light SNP Discovery

Angus

Holstein

Jersey

Hereford

Charolais

Simmental

Brahman

Waygu

high density chip design
High-density chip design
  • >45 million SNPs discovered
  • ~6 million were used to design the high density chip
    • ~800,000 new SNPs added
    • Kept almost all of the BovineSNP50 SNPs
  • Breed groups included
    • Holstein, Angus, Nelore, Taurine dairy, Taurine beef, Indicine, tropically adapted Taurine
  • 852,645 total gaps
    • 850,816 (99.8%) < 20kb
    • 1,795 >20kb, < 100kb
    • 34 > 100 kb
the hd chip in practice
The HD chip in practice
  • 777,962 available SNP
  • 160 bulls genotyped
  • 186,705 SNP edited-out
    • 1,269 unassigned chromosome
    • 3,197 low call rate
    • 1,804 Hardy-Weinberg failures
    • 115,850 MAF < 0.01
    • 64,585 uncertain location
  • 591,258 useable SNP
bovine low density bead chip 3k
Bovine Low-Density Bead Chip (3K)
  • 2,900 SNP
    • Evenly spaced
    • 2,882 useable SNP
    • 14 Y-specific SNP
    • Includes 82 SNP for breed determination
  • Expected to ship very soon
    • Allflex tissue-collection tags to be released
    • Canada will use DNA Genotek nasal swabs
  • Large initial use anticipated
applications of the 3k chip
Applications of the 3K chip
  • Producing AI sires
    • Accuracy adequate for initial screening
    • 50K or HD genotyping for bulls acquired
      • Confirm ID
      • Second-stage selection
    • Genotype more candidates for less money
  • Parentage verification and pedigree discovery
  • Traceability for disease outbreaks
other chips
Other chips
  • 96 SNP parentage chip
    • Use to identify and correct pedigree errors
    • Very low cost
  • 384 SNP chip
    • Use for initial screening of cows
    • 70 to 80% of benefit of 50K for 10% of cost with haplotyping and parental genotypes
  • 700K SNP Affymetrix chip
    • Will be cheaper than Illumina HD chip
illumina chips are mostly nested
Illumina chips are [mostly] nested

Bovine HD (700K)

Missing 7,352 SNP50 markers

Missing 5,264 V2 markers

Bovine SNP50 (50K)

SNP50 v 2 (V2)

50K is missing 14 3K markers

Missing 76 3K markers

Bovine LD (3K)

how do we deal with other chips
How do we deal with other chips?
  • Impute to highest density
  • Calculate SNP effects for all HD SNP
  • Account for loss in accuracy due to imputation error
  • Store only observed genotypes
  • Label evaluations with source of genotype
why impute haplotypes
Why impute haplotypes?
  • Predict unknown SNP from known
    • Measure 3,000, predict 50,000 SNP
    • Measure 50,000, predict 500,000
    • Measure each haplotype at highest density only a few times
  • Predict dam from progeny SNP
  • Increase reliabilities for less cost
how does imputation work
How does imputation work?
  • Identify haplotypes in population using many markers
  • Track haplotypes with fewer markers
  • e.g., use 5 SNP to track 25 SNP
    • 5 SNP: 22020
    • 25 SNP: 2022020002002002000202200
expected rel with haplotyping
Expected REL with haplotyping
  • Actual 3Ksubset of 50K genotypes
    • Correlation (50K, 3K) was .95 to .97
    • REL PA = 35% , 3K = 63% , 50K = 70%
  • Simulated 500K genotypes
    • REL, all animals 50K = 82.6%, 500K = 84%
    • REL improved only if >1,000 had 500K
  • Gains in reliability above PA
    • 3K chip gives >80% of 50K REL gain
    • 50K chip gives >96% of 500K REL gain
whole genome sequencing
Whole-genome sequencing
  • Whole-genome sequences on individuals will be available in the next 5 years
    • How will we store and use those data?
  • Not feasible to calculate SNP effects for 3,000,000,000 SNP
  • Best application may be SNP identification
other genotyping issues
Other genotyping issues
  • Collection of genotypes from universities and public research organization
  • 3K genotypes from cooperator herds need to enter the national dataset for reliable imputation
  • Encourage even more widespread sharing of genotypes across countries
  • Funding of genotyping necessary to predict SNP effects for future chips
  • Intellectual property issues
conclusions
Conclusions
  • The 50K chip has been very successful, but other densities are coming
  • We are collaboratively developing tools to increase the ability to characterize cattle with both lower and higher density SNP chips
  • This technology has the potential to impact the developing world
slide27

Implementation Team

iBMAC Consortium

Funding

  • Illumina (industry)
    • Marylinn Munson
    • Cindy Lawley
    • Diane Lince
    • LuAnn Glaser
    • Christian Haudenschild
  • Beltsville (USDA-ARS)
    • Curt Van Tassell
    • Lakshmi Matukumalli
    • Steve Schroeder
    • Tad Sonstegard
  • Univ Missouri (Land-Grant)
    • Jerry Taylor
    • Bob Schnabel
    • Stephanie McKay
  • Univ Alberta (University)
    • Steve Moore
  • Clay Center, NE (USDA-ARS)
    • Tim Smith
    • Mark Allan
  • AIPL
    • Paul VanRaden
    • George Wiggans
    • John Cole
    • Leigh Walton
    • Duane Norman
  • BFGL
    • Marcos de Silva
    • Tad Sonstegard
    • Curt Van Tassell
  • University of Wisconsin
    • Kent Weigel
  • University of Maryland School of Medicine
    • Jeff O’Connell
  • Partners
    • GeneSeek
    • DNA Landmarks
    • Expression Analysis
    • Genetic Visions
  • USDA/NRI/CSREES
    • 2006-35616-16697
    • 2006-35205-16888
    • 2006-35205-16701
    • 2008-35205-04687
    • 2009-65205-05635
  • USDA/ARS
    • 1265-31000-081D
    • 1265-31000-090D
    • 5438-31000-073D
  • Merial
    • Stewart Bauck
  • NAAB
    • Gordon Doak
    • Accelerated Genetics
    • ABS Global
    • Alta Genetics
    • CRI/Genex
    • Select Sires
    • Semex Alliance
    • Taurus Service

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